Instruments, modules, and methods for improved detection of edited sequences in live cells

Abstract

The present disclosure provides instruments, modules and methods for improved detection of edited cells following nucleic acid-guided nuclease genome editing. The disclosure provides improved automated instruments that perform methods—including high throughput methods—for screening cells that have been subjected to editing and identifying cells that have been properly edited.

We claim: 
     
       1. A solid wall isolation, incubation and normalization (SWIIN) module comprising:
 a retentate member comprising;
 an upper surface and a lower surface and a first and second end, 
 an upper portion of a serpentine channel defined by raised areas on the lower surface of the retentate member, wherein the upper portion of the serpentine channel traverses the lower surface of the retentate member for about 50% to about 90% of the length and width of the lower surface of the retentate member; 
 at least one retentate port fluidically connected to the upper portion of the serpentine channel; and 
 a reservoir cover at the first end of the retentate member; 
 
 a permeate member disposed under the retentate member comprising:
 an upper surface and a lower surface and a first and second end, 
 a lower portion of the serpentine channel defined by raised areas on the upper surface of the permeate member, wherein the lower portion of the serpentine channel traverses the upper surface of the permeate member for about 50% to about 90% of the length and width of the upper surface of the permeate member, and wherein the lower portion of the serpentine channel is configured to mate with the upper portion of the serpentine channel to form the serpentine channel; 
 at least one permeate port fluidically connected to the lower portion of the serpentine channel; and 
 a first and second reservoir at the first end of the permeate member, wherein the first reservoir is fluidically connected to the at least one retentate port in the retentate member and the second reservoir is fluidically connected to the at least one permeate port in the permeate member; 
 
 a perforated member comprising at least 25,000 perforations disposed under and adjacent to the retentate member; 
 a filter disposed under and adjacent to the perforated member and above and adjacent to the permeate member; and 
 a gasket disposed on top of the reservoir cover of the retentate member, wherein the gasket comprises for each of the first and second reservoir a reservoir access aperture configured to provide fluid access to a reservoir and a pneumatic access aperture configured to provide pneumatic access to a reservoir. 
 
     
     
       2. The SWIIN module of  claim 1 , wherein the permeate member further comprises ultrasonic tabs disposed on the raised areas on the upper surface of the permeate member and at the first and second end of the permeate member; the retentate member further comprises recesses for the ultrasonic tabs, wherein the recesses are disposed on the raised areas on the lower surface of the retentate member and at the first and second end of the retentate member; the ultrasonic tabs are configured to mate with the recesses for the ultrasonic tabs; and the permeate member, the retentate member, the perforated member and the filter are coupled together by ultrasonic welding. 
     
     
       3. The SWIIN module of  claim 1 , wherein the permeate member, the retentate member, the perforated member and the filter are coupled together by solvent bonding. 
     
     
       4. The SWIIN module of  claim 1 , wherein the reservoir access apertures receive fluid from outside the SWIIN module or remove fluid from the reservoirs. 
     
     
       5. The SWIIN module of  claim 1 , further comprising a third and a fourth reservoir wherein the third reservoir is 1) fluidically coupled to a second port in the retentate member, 2) fluidically coupled to a third reservoir access aperture in the gasket into which fluids and/or cells flow from outside the SWIIN module into the third reservoir, and 3) pneumatically coupled to a pressure source; and wherein the fourth reservoir is 1) fluidically coupled to a second port in the permeate member, 2) fluidically coupled to a fourth reservoir access aperture in the gasket into which fluids and/or cells flow from outside the SWIIN module into the fourth reservoir, and 3) pneumatically coupled to a pressure source. 
     
     
       6. The SWIIN module of  claim 1 , wherein the perforated member comprises at least 100,000 perforations. 
     
     
       7. The SWIIN module of  claim 6 , wherein the perforated member comprises at least 200,000 perforations. 
     
     
       8. The SWIIN module of  claim 7 , wherein the perforated member comprises at least 400,000 perforations. 
     
     
       9. The SWIIN module of  claim 1 , wherein the retentate member is fabricated from polycarbonate, cyclic olefin co-polymer, or poly(methyl methylacrylate). 
     
     
       10. The SWIIN module of  claim 1 , wherein a serpentine channel portion of each of the retentate and permeate members is from 75 mm to 350 mm in length, from 50 mm to 250 mm in width, and from 2 mm to 15 mm in thickness. 
     
     
       11. The SWIIN module of  claim 1 , wherein a serpentine channel portion of each of the retentate and permeate members is from 150 mm to 250 mm in length, from 100 mm to 150 mm in width, and from 4 mm to 8 mm in thickness. 
     
     
       12. The SWIIN module of  claim 1 , wherein the volume of the mated serpentine channel is from 4 to 40 mL. 
     
     
       13. The SWIIN module of  claim 1 , wherein the volume of a well formed by one of the perforations is from 1 to 5 nL. 
     
     
       14. The SWIIN module of  claim 1 , wherein there is a support on each end of the permeate member configured to elevate the permeate and retentate members above the at least one port in the retentate member and the at least one port in the permeate member. 
     
     
       15. The SWIIN module of  claim 1 , further comprising imaging means to detect cells growing in wells. 
     
     
       16. The SWIIN module of  claim 15 , wherein the imaging means is a camera and a backlight positioned beneath the permeate member. 
     
     
       17. A SWIIN assembly comprising the SWIIN module of  claim 1 , a thermoelectric control device, and a fan. 
     
     
       18. An automated multi-module cell editing instrument comprising:
 the SWIIN module of  claim 1 ; 
 a housing configured to house all of some of the modules; 
 a receptacle configured to receive cells; 
 one or more receptacles configured to receive nucleic acids; 
 a growth module; 
 a cell concentration module; 
 a transformation module configured to introduce the nucleic acids into the cells; and 
 a processor configured to operate the automated multi-module cell editing instrument based on user input and/or selection of a pre-programmed script. 
 
     
     
       19. The automated multi-module cell editing instrument of  claim 17 , wherein the SWIIN module also serves as a recovery module. 
     
     
       20. The automated multi-module cell editing instrument of  claim 17 , wherein the transformation module comprises a flow-through electroporation device.